It’s great to run the user-friendly bioBakery modules! I am new to the shotgun metagenomic field so please let me know if I didn’t describe clearly about my issues.
I ran Humann 3 for my trimmomatic trimmed fastq file (cat merged paired-end). When I took a look at the genefamily.tsv file, I found that there is no organism shown as described in the humann tutorial/manual (https://github.com/biobakery/biobakery/wiki/humann3). Also, the pathway abundance is 0 for unmapped and unintegrated. I was wondering if I missed something when I typed my codes?